title: Genome-wide maps of ERα-bound RNAs.

summary: To identify Estrogen receptor α (ERα) binding sites on RNAs, we performed HITS-CLIP of endogenous ERα.

overall_design: MCF7 cells were subjected to the HITS-CLIP procedure (Licatalosi D, et al. 2008, Nature 456:464-U22)

first: H

last: Goodarzi


title: H3K9me blocks transcription factor activity in differentiated cells to ensure tissue integrity [CUT&RUN; ChICseq]

status: Public on Aug 01 2021

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

summary: Development in multicellular organisms is governed by a carefully orchestrated program of gene expression controlled by both genetic and epigenetic factors1,2. Histone H3 lysine 9 methylation (H3K9me) is the defining modification of heterochromatin, which is thought to have two main functions. It silences satellite repeats and transposable elements to ensure genome stability3, and stabilizes differentiated states by repressing tissue-specific genes4,5. Not surprisingly, the loss of appropriately targeted heterochromatin is associated with cancer, loss of tissue integrity, and aging5-8. How H3K9me restricts transcription is unknown. Here we show that in C. elegans H3K9me2 is required to silence different sets of genes in embryos and differentiated post-mitotic cells. During nematode development H3K9me is lost from genes that define cell-type identity and is gained at genes expressed at prior stages or in alternative tissues. We found that a continuous deposition of H3K9me2 is necessary to maintain silencing in terminally differentiated cells. Its loss leads to DNA decompaction, but this is not sufficient to derepress H3K9me-marked genes. Instead, gene derepression in differentiated tissues requires distinct sets of transcription factors (TF) that aberrantly activate enhancers or promoters. Tissue-specific H3K9me distribution thus contributes critically to cell-type specific TF binding providing a rationale   for how a limited set of TFs can control complex organismal development9,10.

overall_design: ChICseq for H3K9me2, H3K9me3 and H3K27ac from sorted C. elegans L3 larval tissues (body wall muscle) in N2 (Bristol), met-2(n4256) III mutants .

first: Stephen

middle: P

last: Methot

first: Giovanna

last: Brancati

first: Peter

last: Zeller

first: Dimosthenis

last: Gaidatzis

first: Hubertus

last: Kohler

first: Alexander

last: van Oudenaarden

first: Helge

last: Grosshans

first: Susan

middle: M

last: Gasser


title: H3K9me blocks transcription factor activity in differentiated cells to ensure tissue integrity [ATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ATAC-seq from sorted C. elegans L3 larval tissues (body wall muscle, seam cells) in N2 (Bristol), met-2(n4256) III, set-25(n5021) III and met-2(n4256) III; set-25(n5021) III mutants .


title: Maturation signatures of conventional dendritic cell subtypes in COVID-19 suggest direct viral sensing

city: Los Angeles

first: Matteo

last: Pellegrini

address: 405 Hilgard Avenue

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: Growing evidence suggests that conventional dendritic cells (cDCs) undergo aberrant maturation in COVID-19, which negatively affects T-cell activation. The presence of effector T cells in patients with mild disease and dysfunctional T cells in severely ill patients suggests that adequate T-cell responses limit disease severity. Understanding how cDCs cope with SARS-CoV-2 can help elucidate how protective immune responses are generated. Here, we report that cDC2 subtypes exhibit similar infection-induced gene signatures, with the upregulation of IFN-stimulated genes and IL-6 signaling pathways. Furthermore, comparison of cDCs between patients with severe and mild disease showed severely ill patients to exhibit profound downregulation of genes encoding molecules involved in antigen presentation, such as MHCII, TAP, and costimulatory proteins, whereas we observed the opposite for proinflammatory molecules, such as complement and coagulation factors. Thus, as disease severity increases, cDC2s exhibit enhanced inflammatory properties and lose antigen presentation capacity. Moreover, DC3s showed upregulation of anti-apoptotic genes and accumulated during infection. Direct exposure of cDC2s to the virus in vitro recapitulated the activation profile observed in vivo. Our findings suggest that SARS-CoV-2 interacts directly with cDC2s and implements an efficient immune escape mechanism that correlates with disease severity by downregulating crucial molecules required for T-cell activation.

overall_design: Single-cell RNA sequencing of CD11c+ MHCII+ cells isolated from PBMCs of 3 COVID-19 patients and 2 healthy donors.

first: Francesca

last: Granucci

first: Laura

last: Marongiu

first: Giulia

last: Protti


title: Unveiling key players in the Chronic Lymphocytic Leukemia (CLL)-microenvironment interplay

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: Novel dendritic cells (DCs) population in murine bone marrow (BM) that support CLL malignancy

overall_design: Comparison between WT BM DCs to BM DCs in TCL (murine CLL) adoptive transfer model

first: Avital

middle: F

last: Barak

first: Idit

last: Shachar


title: Deciphering the host transcriptional response to SARS-CoV-2 infection

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

summary: SARS-CoV-2 is a beta coronavirus causing COVID-19 which first emerged in Wuhan, China and was later declared a pandemic by the World Health Organization. Since then the economical, health and human cost has been enormous for the world. However, little work has been done to understand the transcriptional changes brought about by the virus in human hosts. We have compared COVID-19 positive samples with negative samples from Indian patients to better understand the host response.. We find many genes related to immune response  up-regulated in the COVID-19 patients. Many of these are the usual response genes against the viral infection but type I interferon appears to be a  key immune response activated against SARS-CoV-2. A large number of the differentially expressed genes were down-regulated pointing towards translational arrest and down regulation of host mRNA during late infection. The down-regulated genes are well correlated with the clinical manifestations and symptoms due to SARS-CoV-2 infection such as the loss of smell and taste. We also find evidence of altered gene expression profiles associated with systemic complications such as neurological disturbances and high insulin requirement. Finally, we have identified many lncRNAs being down-regulated during COVID-19 infections. A few of these lncRNAs have functional role in viral infection. However, to understand the functional role of other lncRNAs, we looked at the function of their closest gene, since lncRNA are believed to have cis functionality. Our analysis suggests a role for lncRNA in down-regulation of metabolic and developmental processes during COVID-19 infection.

overall_design: Differential expression analysis of RNA-Seq data from COVID-19 positive samples against COVID-19 negative control

middle: K

first: Divya

middle: T

last: Sowpati


title: Analysis of mouse central bone marrow versus endosteal transcriptome to define the hematopoietic stem cell niche at the endosteum

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

summary: Stem cell function is regulated by specialized microenvironments called stem cell niches. These niches maintain stem cells in a dormant state and promote self-renewal. The most potent hematopoietic stem cells (HSC) with high self-renewal potential are reportedly enriched in the endosteal compared to the central region of the bone marrow. Therefore we analyzed the global transcriptome of the endosteal region and directly compared it to that of the central bone marrow (BM). This comparative, differential analysis revealed that in addition to genes specific to the  osteoblastic and osteoclastic lineage and classic regulators of HSC (CXCL12, KIT ligand, angiopoietin-1, Jagged-1, N-cadherin), the endosteum abundantly expresses prostaglandin I2 (PGI2) synthase (Ptgis), which produces PGI2. PGI2 is a highly labile, lipid metabolite with no known roles in regulating HSCs. We show in this study that PGI2 is a potent regulator of HSC function. Therefore comparing endosteal versus central BM transcriptome is a viable approach for uncovering candidate genes that may regulate the function of HSC and the HSC niche.

overall_design: Femurs from 3 individual C57BL/6 mice were collected and RNA expression profiles from the central bone marrow and endosteal regions compared. Affymetrix IDs were compared by calculating the log2 of the average endosteal bone marrow signal divided by the average central bone marrow signal.

first: Joshua

last: Tay

first: Valerie

last: Barbier

first: Falak

last: Helwani

middle: R

first: Jean-Pierre

last: Levesque

first: Ingrid

middle: G

last: Winkler


title: Rbfox contributes to a conservative program of self-antigen splicing in thymic epithelial cells [mTEC_bulk_RNAseq]

status: Public on Aug 03 2021

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

summary: Thymic epithelial cells (TEC) guide selection of a T-cell repertoire that is reactive to pathogens but tolerant to self. While this process is known to involve the promiscuous expression of virtually the entire protein-coding gene repertoire by TEC, the extent to which these cells reproduce peripheral isoform structures is unknown. We performed a transcriptomic investigation of transcript structures and splicing factor expression in medullary TEC and 21 peripheral tissues. Our results indicate that TEC re-use a small number of peripheral splicing factors to recreate a limited subset of the peripheral splice isoform repertoire. We found, for example, that TEC lacked both neuronal microexons and the splicing factor, Srrm4, which promotes their inclusion. We demonstrate a functional role for the Rbfox splicing factors in promoting medullary TEC development and the alternative splicing of promiscuously expressed genes. Our findings have implications for understanding autoimmune diseases and the development of antigen-specific immunotherapies.

overall_design: Two biological replicates of four murine mTEC populations were FACS sorted and sequenced from wildtype and Aire knockout mice.

middle: N

first: Kathrin

last: Jansen

first: Georg

middle: A

last: Hollander


title: Hda1C restricts burst frequency to limit divergent non-coding transcription

status: Public on Aug 02 2021

city: Frederiksberg C

first: Maxim

last: Ivanov

address: Thorvaldsensvej 40

department: Dept. of Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

summary: We used Native Elongation Transcript sequencing (NET-seq) to investigate the genome-wide effect of the Hda1 histone deacetylase complex (Hda1C) on the repression of divergent non-coding (DNC) transcription at bidirectional promoters in yeast S.cerevisiae.

overall_design: Native elongating transcripts sequencing (NET-Seq) was used to determine the genomic positions of transcriptionally engaged RNAPII in wild type, hda1Δ and hda3Δ strains.

first: Uthra

last: Gowthaman

first: Isabel

last: Schwarz

first: Heta

last: Patel

first: Niels

last: Müller

first: Desiré

last: García-Pichardo

first: Tineke

last: Lenstra

first: Sebastian

last: Marquardt


title: Next Generation Sequencing Facilitates Quantitative Analysis of Brown adipocytes transcriptomes from Control (LrpprcFF) and LrpprcBKO (LrpprcFF, Ucp1-CRE) mice

city: San Francisco

first: Esther

last: Paulo

state: California

address: 555 Mission Blv South

institute: UCSF

summary: Next-generation sequencing (NGS) brings us the opportunity to analyze cellular pathways. The main goal of this study was to compare brown adipocyte  transcriptome profiling (RNA-seq) between Control and LrpprcBKO mice housed at room temperature or at thermoneutrality.

overall_design: Brown adipocytes mRNA profiles of 8-week old wild type (WT) and LrpprcBKO mice were generated by deep sequencing, in triplicate or quadruplicate, using Illumina HiSeq 2000, by Novogene.

first: Biao

last: Wang


title: Identification of genomic methylation markers for colorectal cancer diagnosis and toxicity of capecitabine-based chemotherapy

city: Shanghai

first: Wansheng

last: Chen

address: 415 Fengyang Road

department: Department of Pharmacy

country: China

institute: Changzheng Hospital, Second Military Medical University

summary: Background: Colorectal cancer (CRC) remains a major concern with high morbidity and mortality worldwide. DNA methylation alteration plays a pivotal role in cancer development. We aimed to screen novel biomarkers for CRC diagnosis and chemotherapy-related adverse event (CRAE) prediction using the advanced Illumina Infinium MethylationEPIC (850K) BeadChip. Methods: We analyzed the methylation profiles of paired tumor and normal tissues from 21 Chinese CRC patients. After normalization by potential confounders, three types of methylation profiles (differentially methylated probes, differentially methylated regions, and gene-function-differentially methylated regions) were further studied by functional annotation and pathway enrichment analysis. At last, integrated-methylation-marker systems for CRC diagnosis and CRAE prediction were developed based on genes within the mostly related pathways and LASSO regression. Findings: Tumor-related methylation was characterized with hypermethylated promoter islands and hypomethylated intragenic openseas. CRAE-related methylation was characterized with hyper- (or hypo-) methylated intragenic (or intergenic) regions. The two most important susceptible factors for various types of CARE were inactive regeneration functions and active immune response. Differentially methylated genes were significantly enriched in neuronal system, metabolism of RNA, and extracellular matrix organization. All of the integrated-methylation-marker systems demonstrated high discriminative accuracy in both CRC diagnosis (AUROC = 1) and CRAE prediction (AUROC = 0.817-1). Interpretation: In this study, we provided new insights on the formation of CRC diagnosis and CRAE based on three types of methylation profile. The integrated-methylation-marker systems combining multiple DMPs were found to have potentially diagnostic and predictive values. Hence, our findings have important clinical implications, and further validation is warranted.

overall_design: Bisulphite converted DNA from the 42 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip

first: Mingming

last: Li


title: Clostridium difficile Biofilm with and without deoxycholate at 48H

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: To understand the molecular mechanisms induced by deoxycholate (DCA) during biofilm formation and to identify factors implicated in the strong density of biofilms in this condition, we performed a transcriptomic analysis using microarrays. The microarrays were used to compare C. difficile transcription profiles of a 48 h biofilm (in BHISG medium) treated with DCA with an untreated biofilm.

overall_design: Two-conditions experiments, 630E strain WT with and without Deoxycholate Biofilm 48h, 4 biological replicates for each condition

first: Thomas

last: Dubois


title: Serum Circulating Proteins from Pediatric Dilated Cardiomyopathy Patients Cause Pathologic Remodeling and Cardiomyocyte Stiffness [Taqman]

status: Public on Jul 31 2021

city: Aurora

first: Danielle

middle: A.

last: Jeffrey

state: CO

department: Pharmacology

institute: University of Colorado

summary: Dilated cardiomyopathy (DCM) is the most common form of cardiomyopathy and main indication for heart transplantation in children. Therapies specific to pediatric DCM remains limited due to lack of a disease model. Our previous study showed that treatment of neonatal rat ventricular myocytes (NRVMs) with non-failing or DCM pediatric patient serum activates the fetal gene program (FGP). Here we show that serum treatment with Proteinase K prevents activation of the FGP, whereas RNase treatment exacerbates it, suggesting that circulating proteins, but not circulating microRNAs, promote these pathological changes. Evaluation of the protein secretome showed that midkine (MDK) is up-regulated in DCM serum, and NRVM treatment with MDK activates the FGP. Changes in gene expression in serum-treated NRVMs, evaluated by next-generation RNA sequencing (RNA-Seq), indicates extracellular matrix remodeling and focal adhesion pathways are upregulated in pediatric DCM serum and serum-treated NRVMs, suggesting alterations in cellular stiffness. Cellular stiffness was evaluated by Atomic Force Microscopy, which showed an increase in stiffness in DCM serum-treated NRVMs. Of the proteins increased in DCM sera, secreted frizzled related protein 1 (sFRP1) was a potential candidate for the increase in cellular stiffness, and sFRP1 treatment of NRVMs recapitulated the increase in cellular stiffness observed in response to DCM-serum treatment. Our results show that serum circulating proteins promote pathological changes in gene expression and cellular stiffness, and circulating miRNAs are protective against pathological changes.

overall_design: Pediatric nonfailing versus dilated cardiomyopathy

first: Julie

last: Da Silva

first: Anastacia

last: Garcia

first: Xuan

last: Jiang

first: Anis

last: Karimpour-Fard

first: Lee

middle: S

last: Toni

last: Lanzicher

first: Brisa

last: Pena

first: Carissa

last: Miyano

first: Karin

last: Nunley

first: Armin

last: Korst

first: Orfeo

last: Sbaizero

first: Matthew

last: Taylor

first: Shelley

last: Miyamoto

first: Brian

middle: L

last: Stauffer

first: Carmen

middle: C

last: Sucharov


title: H3K9me blocks transcription factor activity in differentiated cells to ensure tissue integrity

first: Jan

last: Padeken

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: mRNA expression data of a mouse T-lymphoma cell line WR19L

city: Bunkyou-ku

first: Katsumori

last: Segawa

state: Tokyo

address: 1-5-45, Yushima

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

summary:
Impacts of a point mutation identified in a patient exhibiting developmental and neurological disorders on a phospholipid flippase, ATP11A.
We used microarrays to comprehensively investigate gene expressions which was affected by the mutant ATP11A found in the patient.

overall_design: Parental WR19L, flippase-deficient WR19L (DKO), and DKO cells expressing wild-type or the mutant ATP11A were analyzed on Affymetrix microarrays.

first: Shigekazu

last: Nagata


title: Serum Circulating Proteins from Pediatric Dilated Cardiomyopathy Patients Cause Pathologic Remodeling and Cardiomyocyte Stiffness [SOMA-proteomics]

first: Danielle

last: Jeffrey

first: Julie

last: Da Silva

last: Garcia

first: Thomas


title: H3K9me blocks transcription factor activity in differentiated cells to ensure tissue integrity [RNA-seq]

overall_design: Total RNAseq of RNA isolated from sorted C. elegans L3 larval tissues (body wall muscle, seam cells) in N2 (Bristol), met-2(n4256) III, set-25(n5021) III and met-2(n4256) III; set-25(n5021) III mutants and met-2::degron worms cultured with or without auxin. Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using RNeasy kit (QIAGEN 74104) including DNase treatment. Depletion of ribosomal RNA was done for 5 ľg of total RNA with Ribo-Zero Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator kit (Zymo Research R1015) according to corresponding manufacturers instructions.

first: Stephen

last: Methot

first: Giovanna

last: Brancati

first: Peter

last: Zeller

first: Dimosthenis

last: Gaidatzis

first: Hubertus

last: Kohler

first: Alexander

last: van Oudenaarden

first: Helge

last: Grosshans

first: Susan

last: Gasser


title: Microarray analysis of HeLa Parental vs HeLa radio-resistant tumour xenograft in mice

city: Singapore

first: Dawn

middle: Sijin

last: Nin

address: 8 Medical Drive, Blk MD7, level 4

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: Analysis of differential gene expression in HeLa Parental vs radio-resistant xenograft tumours. The aim is to identify potential genes that are deregulated in radio-resistant tumours.

overall_design: Total RNA obtained from mice HeLa xenograft tumours generated using parental and radio-resistant lines are used for microarray analysis.

first: D

first: C

last: Wujanto

first: T

middle: Z

last: Tan

last: Lim

first: JAM

last: Daman

first: K-Y

last: Wu

first: M

last: Dai

first: Z

middle: W

last: Lee

first: S

last: Idres

first: Y

middle: H

last: Leong

last: Jha

first: JS-Y

last: Ng

first: J

middle: J

last: Low

first: S-C

last: Chang

first: W

first: B

last: Choo

first: L

last: Deng


title: Serum Circulating Proteins from Pediatric Dilated Cardiomyopathy Patients Cause Pathologic Remodeling and Cardiomyocyte Stiffness

first: Danielle

last: Jeffrey

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: mRNA expression profiles of wild-type and CARD10 R587A knock-in A549 cells

city: Basel

first: Anton

last: Glück

country: Switzerland

institute: Novartis Institutes for BioMedical Research

overall_design: 3 replicates each of 3 wild-type A549 clones and 2 CARD10 R587A knock-in A549 clones; 15 samples in total

first: Laura

last: Israël

first: Marjorie

last: Berger

first: Marine

last: Coral

first: Melanie

last: Ceci

first: Adeline

last: Unterreiner

first: Joëlle

last: Rubert

first: Maureen

last: Bardet

first: Stefanie

last: Ginster

first: Alexandra

middle: M

last: Golding-Ochsenbein

first: Kea

last: Martin

first: Thomas

last: Hoyler

last: Calzascia

first: Grazyna

last: Wieczorek

first: Rainer

last: Hillenbrand

first: Stéphane

last: Ferretti

first: Enrico

last: Ferrero

first: Frédéric

last: Bornancin


title: Cardiac fibroblasts regulate macrophage ontogeny, phenotype and function during cardiac injury

city: Baltimore

first: Daniela

last: Cihakova M.D. Ph.D. D(ABMLI)

state: MD

address: 720 Rutland Avenue

department: Pathology-Immunopathology

institute: The Johns Hopkins University School of Medicine

summary: Two types of monocytes, inflammatory and patrolling, infiltrate the hearts in both human myocarditis and murine experimental autoimmune myocarditis (EAM) model. The fates and functions of these infiltrating monocytes governing the progression of heart failure remain unclear. Here, we created parabiotic EAM and naïve mice to show that cardiac inflammation facilitate monocyte-to-macrophage differentiation. Using a combination of flow cytometry, time lapsed imaging and transmission electron microscopy, we demonstrated in vitro that cardiac fibroblasts interact with monocytes and are instrumental in facilitating monocyte-to-macrophage differentiation. Moreover, IL-17A stimulated cardiac fibroblasts completely arrested Ly6Clo monocyte proliferation and inhibited both Ly6Chi and Ly6Clo monocyte-to-macrophage differentiation both in vitro and in vivo after intracardiac injections of monocytes into the hearts. Intriguingly, IL-17A signaling through cardiac fibroblasts also significantly downregulated Mer tyrosine kinase (MerTK) expressions on Ly6Chi monocyte-derived macrophages, thus jeopardizing their phagocytic abilities. Collectively, our results implicate divergent fates and functions of heart-infiltrating monocytes influenced by cardiac fibroblasts.

overall_design: Splenic Ly6Chi monocytes and Ly6Clo monocytes were co-cultured with cardiac fibroblasts with or without IL-17A stimulation for approximately 160 hours, biological triplicates of each conditions that resulted in monocyte-derived macrophages were then FACS sorted and subjected to microarray analysis, total samples n=9

first: Xuezhou

last: Hou

last: Čiháková


title: The SARS-CoV-2 main protease Mpro causes microvascular brain pathology by cleaving NEMO in brain endothelial cells

city: Lübeck

first: Anke

last: Fähnrich

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: LIED

institute: University of Lübeck

summary: COVID-19 can damage cerebral small vessels and cause neurological symptoms. However, the vascular pathology and the  potential  mechanisms are  unclear.  In brains of SARS-CoV-2-infected patients and animal models, we found an increased number of empty basement membrane tubes, so-called string vessels representing remnants of lost capillaries. We obtained evidence that brain endothelial cells are infected and that the main protease of SARS-CoV-2 (Mpro) cleaves NEMO, the essential modulator of NF-κB. By ablating NEMO, Mpro induces the death of human brain endothelial cells and the occurrence of  string  vessels  in  mice.  Deletion  of  receptor-interacting  protein  kinase  (RIPK)  3,  a  mediator  of regulated  cell  death,  blocks  the  vessel  rarefaction  and  disruption  of  the  blood-brain  barrier  due  to NEMO ablation. Importantly, a pharmacological inhibitor of RIPK signaling prevented the Mpro-induced microvascular  pathology.  Our  data  suggest  RIPK  as  a  potential  therapeutic  target  to  treat  the neuropathology of COVID-19.

overall_design: single cell sequencing of the hypothalamus of 10 weeks old wild type mice

first: Helge

last: Müller-Fielitz

first: Fabian

last: Ott

first: Markus

last: Schwaninger


title: DAPT-dependent regulation of zebrafish Muller glial cell chromatin accessibility

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: In this work we identify changes in Muller glial cell chromatin accessibility in response to DAPT-treatment

overall_design: Triplicate samples from gfap:GFP transgenic zebrafish treated with either DMSO or DAPT.

first: Dan

last: Goldman


title: Early life stress affects the miRNA cargo in epididymal extracellular vesicles in mouse

city: Zürich

first: Deepak

last: Tanwar

state: ZH

address: Winterthurerstrasse 190

institute: ETH Zürich

type: Non-coding RNA profiling by high throughput sequencing

summary: Sperm RNA can be modified by environmental factors and has been implicated in communicating signals about changes in a father's environment to the offspring. The RNA composition of sperm is influenced during its final stage of maturation in the epididymis by extracellular vesicles released by epididymal cells. We studied the effect of exposure to stress in postnatal life on the transcriptome of epididymal extracellular vesicles using a mouse model of transgenerational transmission. We found that the small RNA signature of epididymal extracellular vesicles, particularly miRNAs, is altered in adult males exposed to postnatal stress. miRNAs changes correlate with differences in the expression of their target genes in sperm and zygotes generated from that sperm. These results suggest that stressful experiences in early life can have persistent biological effects on the male reproductive tract that may in part be responsible for the transmission of the effects of exposure to the offspring.

overall_design: small RNA sequencing of cauda epididymosomes from 9-month adult, Control or MSUS males. For MSUS, litters were exposed to unpredictable maternal separation combined with unpredictable maternal stress (MSUS) during the first 14 days after birth (Franklin et al., 2010) and for Control, litters were untouched. Control and MSUS males were sacrificed at postnatal-day 28 and at 9-month old for tissue collection.   For cauda epididymosoma sequencing, 5 Control and 5 MSUS samples were used. The sequencing was performed in 2 runs - 1st run without size-selection, 2nd run with miRNA-specific size-selection.

first: Anar

last: Alshanbayeva

first: Martin

last: Roszkowski

first: Francesca

last: Manuella

first: Isabelle

last: Mansuy


title: Virus-induced senescence is a central pathogenic principle and therapeutic target in COVID-19 disease

status: Public on Jul 30 2021

city: Berlin

first: Clemens

last: Schmitt

address: Augustenburger Platz 1

department: Hematology, Oncology, Tumorimmunology

institute: Charite

summary: SARS-CoV-2 infection accounts for COVID-19 lung disease and other organ manifestations. Increasing evidence points towards an inflammatory cytokine network as the underlying driver of actual organ damage and severity of the clinical course. Here we show that SARS-CoV-2, like a broad spectrum of other viruses, evokes cellular senescence as a primary stress response in infected cells, among them respiratory epithelial cells, which is – indistinguishably from other forms of cellular senescence – characterized by typical morphological and cell-cycle arrest features, and accompanied by the massive secretion of largely pro-inflammatory cytokines, termed senescence-associated secretory phenotype (SASP).

overall_design: Examine differentially expressed gene transcripts of senescent cells induced by direct virus infection or conditioned medium from  virus-induced senescent cells.

first: Soyoung

last: Lee

first: Yong

last: Yu

first: Mario

last: Mairhofer

first: Paulina

last: Richter-Pechanska


title: Serum Circulating Proteins from Pediatric Dilated Cardiomyopathy Patients Cause Pathologic Remodeling and Cardiomyocyte Stiffness [RNA-Seq]

first: Danielle

last: Jeffrey

first: Julie

middle: P

last: Da Silva

first: Anastacia

last: Garcia

first: Xuan

last: Jiang

first: Anis

last: Karimpour-Fard

first: Lee

last: Toni

first: Thomas

last: Lanzicher

first: Brisa

last: Pena

first: Carissa

last: Miyano

first: Karin

last: Nunley

first: Armin

last: Korst

first: Orfeo

last: Sbaizero

first: Matthew

last: Taylor

first: Shelley

last: Miyamoto

first: Brian

last: Stauffer

first: Carmen

last: Sucharov


title: DAPT-dependent regulation of zebrafish Muller glial cell gene expression

first: Bioinformatics

last: Core

summary: In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without DAPT for 1 day.

overall_design: Triplicate samples from control DMSO-treated and experimental DAPT-treated gfap:GFP transgenic zebrafish.

first: Dan

last: Goldman


title: Gene expression profiles of Washington navel oranges (Citrus sinensis (L) Osbeck) graft innoculated with Candidatus Liberibacter asiaticus, Spiroplasma citri, or two citrus tristeza isolates

city: Davis

first: Christopher

last: McNeil

state: CA

address: One Shields Ave

institute: University of California Davis

summary: Pathogens can trigger a broad array of changes in gene expression in plants. In this study we report the changes in gene expression patterns that occurred when greenhouse grown Washington Navel oranges (C. sinensis) was graft innoculated with citrus pathogens. Candidatus Liberibacter asiaticus, Spiroplasma citri, and two isolates of citrus tristeza virus were studied.

overall_design: Greenhouse grown Washington navels (C. sinensis (L) Osbeck) were grafted innoculated with Candidatus Liberibacter asiaticus, Spiroplasma citri, or one of two isolates of of citrus tristeza virus: one mild (T30  isolate 07539) and one that causes stem-pitting in susceptible plants (CCTEA-107). Addition trees were graft innoculated with CLas and either of the CTV isolates. Control plants were mock innoculted by recieving grafts of tissue from healthy source plants. Leaf samples were collected 2, 4, and 8 months for RNA extraction and gene expression analysis.

first: Karla

last: Araujo

first: Kristine

last: Godfrey

first: Carolyn

last: Slupsky


title: DN-MAML-dependent regulation of zebrafish Muller glial cell gene expression

summary: In this work we identify genes differentially expressed in Muller glia from uninjured retina in zebrafish treated with and without DN-MAML for 1 day.

overall_design: Triplicate samples from control heat shock-treated gfap:GFP transgenic zebrafish and heat shock-treated gfap:GFP;hsp70:DN-MAML transgenic zebrafish.


title: Injury-dependent regulation of zebrafish Muller glial cell chromatin accessibility

summary: In this work we identify changes in Muller glial cell chromatin accessibility in response to retinal injury

overall_design: Triplicate samples from control uninjured and experimental needle poke injured gfap:GFP transgenic zebrafish.


title: Notch signaling and Muller glia's regenerative response


title: RNA-sequencing of BCL6-sufficient and -insufficient OT-II TFH cells

city: Beijing

first: Hai

last: Qi

state: Non-US/Non-Canadian

address: Shuangqing Road

institute: Tsinghua University

summary: We analyzed the transcriptome differences of BCL6-sufficient (CD4-Cre) and -insufficient (CD4-CrexBcl6fl/+) OT-II TFH cells. CD4-CrexBcl6fl/+ or control CD4-Cre OT-II T cells were transferred into CD45.1 Sap-/- mice. At day 3 post NP-OVA immunization, CXCR5hiPD-1hi TFH cells were sort-purified from the draining lymph node and prepared for RNA-seq analysis. Two technical repeats of ~200 cells per sample from each of 3 mice were included. BCL6-insufficient TFH cells differentially expressed many genes; among those downregulated were Stim1 and Plcg1, which code for STIM1 and PLCg1, respectively, that both impinge on calcium signaling downstream of TCR activation. Moreover, KEGG pathway analyses revealed that the calcium signaling-related pathway was generally upregulated in wildtype as compared to BCL6-insufficient TFH cells. These data support the notion that BCL6 control follicular T-B interactions by regulating multiple target genes involved in antigen-triggered calcium signaling in T cells.

overall_design: Transcriptome analysis of CD4-CrexBcl6fl/+ or CD4-Cre OT-II TFH cells 3 days after activation in vivo by NP-OVA immunization

first: Jiahui

last: Sun

first: Ye

last: Li

last: Liu

first: Jiacong

last: Yan

first: Bo

first: Weiwei

last: Ma

first: Xingxing

last: Shao


title: Cand2 links pathological mTORC1 signaling to adverse cardiac remodeling by regulating Grk5 expression

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: The mechanistic target of rapamycin (mTOR) is a key regulator of pathological remodeling in the heart by activating ribosomal biogenesis and mRNA translation. Inhibition of mTOR in cardiomyocytes is protective, however, a detailed role of mTOR in translational regulation of specific mRNA networks in the diseased heart is largely unknown. A cardiomyocyte genome-wide sequencing approach was used to define mTOR-dependent post-transcriptional gene expression control at the level of mRNA translation. This approach identified the muscle specific protein Cullin-associated NEDD8-dissociated protein 2 (Cand2) as a translationally upregulated gene dependent on the activity of mTOR. Deletion of Cand2 protects the myocardium against pathological remodeling. Mechanistically, we found that Cand2 links mTOR- signaling to pathological cell growth by increasing Grk5 protein expression. Our data suggest that cell-type specific targeting of mTOR might have therapeutic value for adverse pathological cardiac remodeling.

overall_design: Comparision of WT mice vs global Cand2 KO mice

first: Mirko

last: Völkers


title: cis-regulation of Grem1 expression during limb development [E10.5 H3K27Ac ChIP-Seq]

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. The BMP antagonist Gremlin1 (Grem1) is an important node in the gene regulatory network that controls vertebrate limb development. In this study, we used a combination of open chromatin profiling (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) in mouse and chick to identify putative cis-regulatory modules (CRMs) that regulate Grem1 in limb buds. Using CRISPR/Cas genome editing we generated different Grem1 regulatory alleles lacking either individual CRMs, combinations or entire enhancer clusters. To study potential interactions of these CRMs with the Grem1 promoter, we generated 4C-seq profiles of specific regulatory alleles. Taken together our results revealed that the spatio-temporal changes in Grem1 expression are caused by cis-regulatory alterations due to the deletions of enhancer clusters rather than global changes in chromatin architecture.

overall_design: Chromatin immunoprecipitation was performed on the distal part of  E10.5 forelimbs of wild type mice.

first: Rushikesh

last: Sheth

first: Rolf

last: Zeller

first: Aimee

last: Zuniga

first: Florian

last: Geier


title: Genetic dissection of a super enhancer controlling the Nppa-Nppb cluster in the heart

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

overall_design: Refer to individual Series


title: Haploinsufficiency of BCL6 impairs follicular T-B interactions


title: Single cell transcriptome analysis (scRNASeq) and inferred single cell copy number variations (scCNVs) of cancer associated fibroblast (CAFs) populations in murine KPC pancreatic tumors

status: Public on Jul 29 2021

city: Frederick

first: Yongmei

last: Zhao

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

summary: To study possible CNVs and genes affected by CNVs in the cancer associated fibroblast populations of pancreatic cancers, we applied single cell sequencing technology (10x Genomics) to identify different subpopulations in murine KPC pancreatic tumors and pancreata of age- and gender-matched non-tumor bearing mice. Single cell RNA sequencing (scRNA-Seq) identified three major CAF subpopulations which were interrogated together with the ductal carcinoma population for CNVs using a previously reported inferCNV algorithm. Fibroblasts and ductal cells identified by scRNA-Seq in normal, uninvolved pancreas were used as reference and inferCNVs in both CAF and ductal carcinoma cells were validated with CNVs previously reported within a large high-resolution array comparative genomic hybridization (aCGH) of KPC tumors. CNVs were exclusively detected in the myelofibroblastic cancer associated fibroblast (myCAF) subpopulation and not in the other CAF phenotypes. In comparison to ductal carcinoma cells, myCAFs were less frequently affected by CNVs. CNVs in the myCAFs which were unique for the myCAFs and not shared with gene loci affected by CNVs in ductal carcinoma cells included known regulators of CAF activation, CAF-mediated cancer cell invasion, or antagonists of TGFβ signaling.

overall_design: Single cell RNAseq of murine KPC pancreatic tumors and uninvolved pancreas

first: Robert

last: Stephens

first: Monika

last: Mehta

first: Keyur

last: Talsania

first: Vicky

last: Chen

first: Parimal

last: Kumar

first: Bao

last: Tran

first: Dandan

first: Serguei

last: Kozlov

first: Udo

last: Rudloff


title: Genetic dissection of a super enhancer controlling the Nppa-Nppb cluster in the heart after cardiac stress

summary: High-resolution chromosome conformation capture-sequencing of wildtype mice left ventricle after cardiac stress (i.e. hypertrophy and myocardial infarction)

overall_design: 4C sequencing on left ventricle of 8-12 weeks old mice

first: Joyce

last: Man


title: Single Cell RNA for in vitro neural tube

city: Santa Barbara

first: Eyal

last: Karzbrun

address: UCSB

department: Physics

institute: UCSB

summary: We analyze single cell RNA in a human stem cell system that recapitulates neural tube folding morphogensis.

overall_design: Droplet-based single-cell RNA sequencing was performed on dissociated cells from iPSC-derived structures recapitulating human neurulation at four timepoints of the differentiation protocol (24h, 48h, 72h, 120h) using the Chromium Single Cell Kit v3.1 (10x Genomics)

first: Stella

middle: K

last: Glasauer

first: Sebastian

last: Streichan


title: RNA-sequencing of pre-GC B cells helped by CD4-CrexBcl6fl/+ or CD4-Cre OT-II T cells

first: Hai

last: Qi

summary: We analyzed transcriptome differences of antigen-specific pre-GC B cells. We transferred wildtype (CD4-Cre) or BCL6-insufficient (CD4-CrexBcl6fl/+) OT-II T cells into SAP-deficient mice and immunized these mice with NP-OVA. By day 3 post immunization, we sort-purified NP-binding B cells that were developing into GCs and conducted RNA-seq analyses of their transcriptome. NP+IgDlowB220+ pre-GC B cells from recipients of the same group were pooled to sort-purify 4 200-cell repeats. Using a gene expression signature induced by CD40 signaling in B cells for enrichment analysis, we found such CD40-induced gene set expression was significantly deprived in those NP-binding B cells helped by CD4-Cre´Bcl6fl/+ T cells. These data suggest BCL6 insufficiency in T cells leads to impaired CD40L signaling to B cells.

overall_design: Transcriptome analysis of pre-GC B cells helped by CD4-CrexBcl6fl/+ or CD4-Cre OT-II T cells 3 days after activation in vivo by NP-OVA immunization.

first: Jiahui

last: Sun

first: Ye

last: Li

first: Dan

last: Liu

first: Jiacong

last: Yan

first: Bo

first: Weiwei

last: Ma

first: Xingxing

last: Shao


title: Genetic dissection of a super enhancer controlling the Nppa-Nppb cluster in the heart of RE3 mutants

first: Vincent

last: Christoffels

summary: High-resolution chromosome conformation capture-sequencing of RE3 homozygous mutants

overall_design: 4C sequencing on left ventricle of 8 week old mice


title: Transcriptomic profiling of MDA-MB-231 cells treated with sub-lethal concentrations of Wild Yam Root Extract (Dioscorea Villosa)

status: Public on Jul 26 2021

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

summary: Background/Aim:   Our previous in vitro high throughput (HTP) botanical anticancer cytotoxic screenings indicated that the wild yam extract (Dioscorea villosa (WYE)) has very potent anticancer effects in terms of espousing cell death with a low IC50 across diverse cancer cell lines including glioblastoma, melanoma, colon, neuroblastoma, and breast.   However, unlike other botanicals we have focused on, WYE contains a high content of detergent steroidal saponins. As surfactants, they act by direct contact to rapidly reduce oil-water interfacial tensions causing disintegration of bio-lipid membranes.  This study examined the WYE at sub-lethal concentrations where the saponin content does not create an interfering variable of lytic cell death in MDA-MB-231 triple-negative breast cancer (TNBC) cells. Methods:  A method validation study was first set up to cross-confirm the inverse relationship between saponin content with lytic cell death, where saponins were associated with loss of plasma and mitochondrial membrane potential and cytotoxic effects in both 2D and 3D cultures. Once appropriate sub-lethal concentrations were established, we then monitored changes in whole transcriptomic (WT) mRNA, miRNA, and long intergenic non-coding RNAs and cross- confirm this data by cell proliferation studies spot test antibody-protein arrays, and ELISA. Results:  Upregulated DEGS reflected immune-stimulating effects centering on TNF signaling, COX2, cytokine release, and   cholesterol/steroid biosynthesis. Downregulated DEGs show a very different transcriptome signature, revealing severe, extensive damage to cell cycle processes, including loss of transcripts for cell division cycle (CDC) genes (25A,45,6,7, A2, A7, A7L,8) cyclins (CCN.) (A2, B1, B2, E2, F) as well as cyclin-dependent kinases (CDKs), centromere proteins (CENP), kinesin family members (KIFs), and polo-like kinases (PLKs) with exception to a corresponding upregulated DEG for p21 gene CDKN1A, all which were corroborated by the cytostatic effects confirmed during a 6-day proliferation study. Conclusions:  In conclusion, WYE appears to mediate a saponin lytic effect at high concentration on direct contact, however at lower concentrations and independent of cell death, there exist three distinct biological consequences as found in this breast cancer cell model, including pro-inflammatory, steroid biosynthetic, and collapse of the cell cycle.

overall_design: The effects of Wild Yam Root (crude) Extract at sublethal concentrations, on MB-231 cells evaluated by whole transcriptome: including mRNAs and long intergenic non-coding RNA transcripts using GeneChip™ Human Gene 2.1 ST Arrays by Affymetrix Inc.

first: Karam

middle: F

last: Soliman


title: cis-regulation of Grem1 expression during limb development [E11.5 H3K27Ac ChIP-seq]

first: DBM Bioinformatics

last: Core Facility

overall_design: Chromatin immunoprecipitation was performed on the distal part of  E11.5 forelimbs of wild type mice.

first: Rushikesh

last: Sheth

first: Rolf

last: Zeller

first: Aimee

last: Zuniga

first: Florian

last: Geier


title: cis-regulation of Grem1 expression during limb development [ATAC mouse forelimb buds]

overall_design: ATAC-seq analysis on dissected E9.75 mouse forelimb buds

first: Javier

last: Lopez-Rios


title: cis-regulation of Grem1 expression during limb development [ATAC HH24]

overall_design: ATAC-seq analysis on dissected HH24 chick wing buds


title: Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

city: Nanning

first: Lei

last: Zhou

state: Guangxi

address: Daxuedong Road, Xixiangtang District

department: College of Animal Science and Technology

institute: Guangxi university

summary: Luchuan pig is a typical obese pig breed in China, and the diameter and area of its longissimus dorsi muscle fibers are significantly smaller than those of Duroc (lean) pig. Skeletal muscle fiber characteristics are related to meat quality of livestock. The smaller the diameter and area of muscle fiber, the better the meat quality. The diameter and area of muscle fibers are related to muscle growth and development. Therefore, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to investigate the potential mechanism underlying the difference in skeletal muscle growth and development between the two types of pigs. First, transposase-accessible chromatin was analyzed to map the landscape of open chromatin regions and transcription factor binding sites. We identified several transcription factors that potentially affected muscle growth and development, including TFAP4, MAX, NHLH1, FRX5, and TGIF1. We also found that transcription factors with basic helix-loop-helix structures had a preference for binding to genes involved in muscle development. Then, by integrating ATAC-seq and RNA-seq, we found that the Wnt signaling pathway, the mTOR signaling pathway, and other classical pathways regulate skeletal muscle development. In addition, we found some pathways that might regulate skeletal muscle growth, such as parathyroid hormone synthesis, secretion, and action, synthesis and degradation of ketone bodies, and the thyroid hormone signaling pathway, which were significantly enriched. After further study, we identified a number of candidate genes (ASNS, CARNS1, G0S2, PPP1R14C, and SH3BP5) that might be associated with muscle development. We also found that the differential regulation of chromatin openness at the level of some genes was contrary to the differential regulation at the level of transcription, suggesting that transcription factors and transcriptional repressors may be involved in the regulation of gene expression. Our study provided an in-depth understanding of the mechanism behind the differences in muscle fibers from two species of pig and provided an important foundation for further research on improving the quality of pork.

overall_design: Transposase-accessible chromatin and mRNA of longissimus muscle of 180-day-old Duroc and Luchuan pigs.

last: Miao

first: Zeqiang

first: Zhanyang

last: Tang

first: Lin

last: Yu

first: Siqi

first: Tengda

last: Huang

first: Peng

last: Wang

first: Tian

last: Wu

first: Ziyi

last: Song

first: Haojie

last: Zhang

first: Yixing


title: MOF haploinsufficiency triggers diet-induced obesity resistance

status: Public on Jul 23 2021

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: This SuperSeries is composed of the SubSeries listed below.


title: Transcriptomic analyses of cardiomyopathy development in mice carrying the phospholamban p.(Arg14del) pathogenic variant, and comparison with ischemic heart disease

status: Public on Jul 22 2021

city: Utrecht

first: Cornelis

middle: J.

last: Boogerd

address: Uppsalalaan 8

department: Developmental Biology and Stem Cell Research

institute: Hubrecht Institute

summary: Background: The p.(Arg14del) pathogenic variant (R14del) of the phospholamban (PLN) gene is a prevalent cause of cardiomyopathy with heart failure. The exact underlying pathophysiology is unknown, and a suitable therapy is unavailable. We aim to identify molecular perturbations underlying this cardiomyopathy in a clinically relevant PLN-R14del mouse model. Methods: We investigated progression of cardiomyopathy in PLN-R14∆/∆ mice using echocardiography, electrocardiography and histological tissue analysis. RNA sequencing and mass spectrometry were performed on cardiac tissues at 3 weeks of age (before onset of disease), 5 weeks (mild cardiomyopathy), and 8 weeks (end-stage). Data were compared with cardiac expression levels of mice that underwent myocardial ischemia-reperfusion or myocardial infarction surgery, in an effort to identify alterations that are specific to PLN-R14del-related cardiomyopathy. Results: At 3 weeks of age, PLN-R14∆/∆ mice had normal cardiac function, but from the age of 4 weeks, we observed increased myocardial fibrosis and impaired global longitudinal strain. From 5 weeks onwards, ventricular dilatation, decreased contractility and diminished electrocardiogram voltages were observed. Strikingly, PLN protein aggregation was present prior to onset of functional deficits. Transcriptomics and proteomics revealed differential regulation of processes involved in remodeling, inflammation and metabolic dysfunction, in part similar to ischemic cardiomyopathy. Altered protein homeostasis pathways were identified exclusively in PLN-R14∆/∆ mice, even before disease onset, in concert with aggregate formation. Conclusions: We mapped the development of PLN-R14del-related cardiomyopathy, and identified alterations in proteostasis and PLN protein aggregation amongst the first manifestations of this disease, which could possibly be a novel target for therapy.

overall_design: RNA-Seq on mouse hearts from WT and phospholamban (Pln) R14del mutant mice (3, 5, or 8 weeks old), and ischemic heart diease induced by ischemia-reperfusion (I/R) injury, myocardial infarction (MI) or sham surgery (n=4/group).

first: Tim

middle: R

last: Eijgenraam

first: Eva

last: van Rooij

first: Herman

last: Silljé

first: Rudolf

last: de Boer


title: CHIP-Seq analysis of CREB1 binding after ALVAC vaccination in Human PBMC

status: Public on Jul 25 2021

city: Blainville

first: Adam-Nicolas

last: Pelletier

state: Quebec

address: 97, Montcalm

country: Canada

institute: RPM Bioinfo Solutions

summary: The RV144 HIV vaccine trial remains the only study to demonstrate significant protection from future HIV-1 acquisition. One of the key components of the RV144 vaccine was the use of the canarypox vector ALVAC as the priming component. Since AIDSVAX, the booster component, alone failed to provide protection we hypothesized that the ALVAC prime contributed significantly to the generation of protection. To test this, we designed a NHP immunogenicity trial to mechanistically link ALVAC vaccination with the magnitude of V1V2 titers, the most significant immune correlate of reduced HIV-1 acquisition in RV144. Our objective was to use a systems biology approach to identify the transcription factors, target genes and immune pathways which were being induced by ALVAC vaccination and associated with higher V1V2 titers. We identified the transcription factor CREB1 and its target genes as rapidly induced by ALVAC in multiple immune subsets and that CREB1 drives the expression and activation of a network of other TFs which are critical for modulating immune responses. Pathways induced by this ALVAC-CREB1 axis include lymphocyte/leukocyte migration, lymphocyte differentiation, antigen processing and presentation, T cell co-stimulation and cytokine signaling.

overall_design: PBMCs were infected in vitro with an MOI 10:1 of ALVAC-HIV, with media cultured cells as a control.  ALVAC-infected PBMCs were compared with media condition at 24 hours after CREB1 chromatin immunoprecipitation.

first: Jeffrey

middle: A

last: Tomalka

first: Slim

last: Fourati

first: Muhammad

middle: B

last: Latif

first: Ashish

last: Sharma

first: Kathryn

last: Furr

first: Kevin

last: Carlson

first: Michelle

last: Lifton

first: Ana

last: Gonzalez

first: Peter

last: Wilkinson

first: Genoveffa

last: Franchini

first: Robert

last: Parks

first: Norman

last: Letvin

first: L

middle: Y

last: Nicole

first: E

last: Kelly

first: Georgia

last: Tomaras

first: Jim

last: Tartaglia

first: Merlin

last: Robb

first: Nelson

last: Michael

first: Richard

last: Koup

first: Barton

last: Haynes

first: Sampa

last: Santra

first: Rafick-Pierre

last: Sékaly


title: MOF haploinsufficiency triggers diet-induced obesity resistance (ChIP-seq)

first: Asifa

last: Akhtar

summary: Constant crosstalk between epigenetic regulators and metabolism homeostasis ensures that several tissues can respond and adapt to environmental cues. Decreased levels of the lysine acetyltransferase (KAT), MOF, was recently associated with cerebral development and syndromic intellectual disability. However, the consequences of having a chronic reduction of MOF levels are still unveiled. Here we characterized by FIA-MS/MS the metabolic profile of Mof heterozygous animals. We generated the profile of 7 different organs that have distinct metabolic demands. Overall our analysis reveled that Mof heterozygous mice have impaired glucose homeostasis, fatty acids metabolism, and amino acid accumulation. Furthermore, when exposed ad libitum to high-fat diet those animals failed to gain fat mass, while the lean mass remains unalterable. Accordingly, at the molecular level, using the adipocyte model we found that Mof regulates the expression of PPARs and Slc2a4. In summary, we identified the first KAT that shows high-fat diet resistance and we propose that the chronic reduction of Mof has a strong impact on metabolic disorders.

overall_design: Experimental design: Visceral white adipocyte (WAT) from 2 control and 3 Mof +/- was extracted. WAT of 8 week old SD treated animals was minced and transferred into a Dounce homogenizer (loose pestle), covered with 1% formaldehyde in PBS, and dissociated, followed by 15 min incubation at room temperature (RT). During incubation, the tissue suspension was filtered using a nylon 70 µM cell strainer (Falcon, 352350). 125 mM glycine final was added to the sample, incubated at RT for 5 min and the suspension was pelleted for 5 min at 500 g. Cell pellets were washed twice in ice cold PBS and pelleted for 5 min at 500 g. For NEXON based nuclei isolation cell pellets were resuspended in 1ml of lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal, protease inhibitor cocktail. Cell suspension was transferred into Covaris MilliTube (cat. No. 520130) and sonicated in Covaris instrument (E220) for 30 sec at peak power 75W, duty factor 10% and 200 cycles/burst. Nuclei were pelleted at 1000g at 20°C for 5min. Pellets were resuspended in 0.5% SDS and incubated at RT for 10min. Sample was diluted 1:5 in the digestion buffer (1.1% Triton, 1x CutSmart buffer , H2Odest). Up to 1*10^6 nuclei were digested with Cvik1 (5U/100.000 cells) at 25°C for 17hrs, shaking at 800rpm. Nuclei were pelleted for 5min at 1000g and washed in a nuclei wash solution (10mM Tris-HCl pH 8, 0.25% Triton, 0.2mg/ml BSA ) until residual fat was removed. Nuclei were pelleted at 5000g for 10min, resuspend in the shearing buffer (10mM Tris-HCl pH 8, 0.1% SDS, 1mM EDTA), transferred into Covaris MicroTube (cat. No. 520052) and sonicated for 6min at peak power 105W, duty factor 2% and 200 cycles/burst. Sample was diluted 1:6 in 1x iC1 buffer (iDeal ChIP-seq, Diagenode) and incubated with 2ug of antibody o/n at 4°C. The next day protein G Dynabeads were added and incubated for 3 hrs at 4°C. Beads were washed and DNA was eluted according to manufacturer's instructions (iDeal ChIP-seq, Diagenode). DNA was purified using MinElute PCR purification kit (Qiagen) for further analysis.


title: MOF haploinsufficiency triggers diet-induced obesity resistance (RNA-seq)

summary: Constant crosstalk between epigenetic regulators and metabolism homeostasis ensures that several tissues can respond and adapt to environmental cues. Decreased levels of the lysine acetyltransferase (KAT), MOF, was recently associated with cerebral development and syndromic intellectual disability. However, the consequences of having a chronic reduction of MOF levels are still unveiled. Here we characterized by FIA-MS/MS the metabolic profile of Mof heterozygous animals. We generated the profile of 8 different organs that have distinct metabolic demands. Overall, our analysis revealed that Mof heterozygous mice have impaired glucose homeostasis, fatty acids metabolism, and amino acid accumulation. When exposed ad libitum to high-fat diet those animals failed to gain fat mass, while the lean mass remains unalterable. At the molecular level, using the adipocyte model we found that Mof regulates the expression of PPARs and Slc2a4. In summary, we identified the first KAT that shows high-fat diet resistance and we propose that the chronic reduction of Mof impacts metabolic disorders.

overall_design: Wild type (control) and Mof heterozygous animals (het) were fed with either standart diet or high fat diet. To understand the intrisic role of Mof in redulating adipocyte whithe adipocyte tissue from 8 weeks-old animals under SD were sample and bulk RNAseq was performed. While to understand how diet would be affected we analyzed the transcriptome profile from WATof 27 weeks-old animals having HFD for 20 weeks. Experimentally, visceral white adipocyte tissue (WAT) was weighed and an equal amount of tissue was lysed directly in TRIZOL and samples were homogenized using an electric tissue homogenizer. Then, samples were incubated with 95% EtOH and transferred into mini-kit RNA extraction Zymo kit (R1054) and pure total RNA was extracted according to the manufacturer’s instructions. RNA concentrations were quantified on a Qubit 2.0 Fluorometer (Life Technology) and quality for deep sequencing checked by Fragment analyzer. after quality control was then used to generate libraries using Illumina TruSeq RNA Sample Prep v2 (RS-122-2001). The manufacturer’s recommendations were followed and the libraries were sequenced on an Illumina NovaSeq6000 sequencer. All sequence data were performed in 3 biological replicates for SD group and duplicates for HFD group. The reads were conducted at 2 x 100 bp length.

first: Cecilia

last: Rodrigues


title: Exploring a novel target of levetiracetam to suppress microglial inflammatory reaction

status: Public on Jul 28 2021

city: Higashi-Hiroshima

first: Yasuhiro

last: Ishihara

state: Hiroshima

address: 1-7-1 Kagamiyama

department: Graduate School of Integrated Sciences for Life

institute: Hiroshima University

summary: Microglia are macrophages-like cells in the central nervous system (CNS) harboring important roles such as synaptic organization, phagocytosis of debris and apoptotic cells, and repairing damaged tissue. Microglial function is tightly controlled, but under certain pathological conditions, activated microglia can induce excess inflammation which injure live cells in the CNS. Therefore, suppression of microglia is a fundamental strategy to treat CNS disorders. We have previously shown that the antiepileptic drug levetiracetam (LEV) inhibits microglia activation, but mechanism remains unclear. The purpose of this study is to identify a target of LEV to suppress microglial activity.

overall_design: BV-2 cells were pretreated with levetiracetam and then treated with lipopolysaccharide.

first: Kouji

last: Niidome

first: Ruri

last: Taniguchi


title: RNA-Seq analysis of prostate cancer cells after 3-bromopyruvic acid treatment

status: Public on Jul 21 2021

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: We performed RNA-seq analysis using differnt prostate cancer cell lines (PC3 and LNCaP) after 3-bromopyruvic acid treatment. We reported that 3-bromopyruvic acid regulatescell cycle-associated genes in PC3 cells. 3-bromopyruvic acid induces apoptosis and suppresses cell cycle progration, cell migration and invasion in PC3 cells.

overall_design: Examination of mRNA profile of differnt prostate cancer cell lines (PC3 and LNCaP) under 3-bromopyruvic acid treatment.

first: Chia-Yang

last: Li


title: Seminal Plasma and Extracellular Vesicles of Aged Male Mouse affects Early embryo Implantation via immunomodulation

status: Public on Jul 27 2021

city: Nanjing

first: Dandan

last: Wang

state: Jiangsu

address: 305 East Zhongshan Road

department: Department of Reproductive Medicine

institute: Affiliated Jinling Hospital, Medicine School of Nanjing University

summary: The seminal plasma (sp), especially the extracellular vesicles of seminal plasma (sEV) which change with age can affect the endometrial immune microenvironment of female mice. However, it is unclear whether the decline in fertility of reproductively old males is related to the alterations of the sp and sEV which may have compromised effect on the immune microenvironment of the female uterus. In this research, we found a decrease in the implantation rate of pseudo-pregnant female mice which was treated with sp from reproductively old male mice (aged-sp group) than sp from young male mice (young-sp group). RNA-sequence analysis revealed an increase in the expression level of local cytokines and chemokines in the uterus of aged-sp groups than those of young-sp groups. Further in vitro experiments found an induction of dendritic cells (DC) maturation in the aged-sp groups. After isolating and characterizing sEV in young and aged male mice, we perfused the uterus of aged-sp group with sEV from young male mice and found it could partially rescue the low implantation rate of the aged-sp group. Further in vitro experiments found an induction of DC maturation after treating with sEV from aged male mice than that from young male mice, which indicated an age-related activation effect of sp and sEV. In conclusion, we found sp and sEV from aged male mice could induce the maturation of DC, which compromised the microenvironment of female reproductive tract, therefore leading to a decrease in implantation rate.

overall_design: Uterine mRNA profiles of pseudopregnant female mice 3.5 days after caged with young and old ligated male mice.

first: Jueraitetibaike

last: Kadiliya


title: Microarray analysis of correlates of vaccine immunogenecity following ALVAC vaccination in NHP in Study 36

first: Adam-Nicolas

last: Pelletier

overall_design: Study 36 was an immunogenicity study designed to test the impact of ALVAC priming on the magnitude and durability of V1V2 antibody responses. There were 2 experimental arms, each comprised of 5 Chinese-origin Rhesus macaque. Both arms used 2 primes with ALVAC and 2 boost with ALVAC + gp120 B/E protein. In Arm I, the ALVAC vector contained no HIV DNA insert which is referred to as empty ALVAC. In Arm II, the ALVAC vector contained the vCP1521 insert which was used in RV144 and encodes for HIV gag, pol and env. Vaccine administration schedule was: Prime 1 in Week 0, Prime 2 in Week 4, Boost 1 in Week 12 and Boost 2 at Week 23. PBMCs were isolated at 2-3 days post Prime 1, 2-weeks post Prime 1 and 2-weeks post Boost 2. DCs, CD4+ T cells and B cells were sorted using flow cytometry and RNA extracted from each sorted subset. V1V2 antibody titers were quantified at four timepoints: Week 14, Week 25, Week 53 and Week 55.

first: Jeffrey

last: Tomalka

first: Slim

last: Fourati

first: Muhammad

last: Latif

first: Ashish

last: Sharma

first: Kathryn

last: Furr

first: Kevin

last: Carlson

first: Michelle

last: Lifton

first: Ana

last: Gonzalez

first: Peter

last: Wilkinson

first: Genoveffa

last: Franchini

first: Robert

last: Parks

first: Norman

last: Letvin

first: Nicole

middle: L

last: Yates

first: Kelly

middle: E

last: Seaton

first: Georgia

last: Tomaras


title: cis-regulation of Grem1 expression during limb development

city: Basel

first: DBM Bioinformatics

last: Core Facility

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus

overall_design: Refer to individual Series


title: Genome-wide mapping of 5-hydroxymethyluracil in Trypanosoma brucei

status: Public on Jul 11 2021

city: Wuhan

first: chengjie

last: ma

address: luojiashan street 16

institute: Wuhan University

summary: 5-Hydroxymethyluracil (5hmU) is a thymine modification existing in the genomes of a number of living organisms. The post-replicative formation of 5hmU occurs via hydroxylation of thymine, which can be mediated by the ten-eleven translocation (TET) dioxygenases in mammalian and J-binding proteins (JBPs) in protozoan genomes, respectively. In addition, 5hmU also can be generated through oxidation of thymine by reactive oxygen species or from deamination of 5hmC by activation-induced cytidine deaminase (AID) or APOBEC family enzymes. While the biological roles of 5hmU have not been fully explored, identifying its genomic location will assist in elucidating its functions. Herein, we report a method of enzyme-mediated bioorthogonal labeling to selectively enrich genomic regions containing 5hmU. 5hmU DNA kinase (5hmUDK) was utilized to selectively install an azide group or alkynyl group into the hydroxyl group of 5hmU followed by incorporation of the biotin linker through click chemistry and capture of 5hmU-containing DNA fragments via streptavidin pull-down. The enriched fragments were applied to deep sequencing to map the location of 5hmU. With this established enzyme-mediated bioorthogonal labeling strategy, we achieved the genome-wide mapping of 5hmU in Trypanosoma brucei (T. brucei) genomes. The method described here will allow for a better understanding of the functional roles and dynamics of 5hmU in genomes

overall_design: Mapping of 5-hydroxymethyluracil DNA modification in Trypanosoma brucei

first: Cheng-Jie

last: Ma

first: Lin

last: Li

first: Wen-Xuan

last: Shao

first: Jiang-Hui

last: Ding


title: RNAseq of hnRNPC and ADAR deficient THP-1

status: Public on Jul 16 2021

city: Biberach a.d. Riß

first: Anna-Maria

last: Herzner

address: Birkendorfer Str 65

institute: Boehringer Ingelheim

summary:
Endogenous double-stranded RNA is prevented from activating the cytosolic antiviral receptor MDA5 by adenosine-to-inosine editing by ADAR. Consequently, CRISPR/cas9 targeting ADAR in the human monocytic cell line THP-1 induces a spontaneous MDA5-dependent interferon response. This response is synergistically enhanced by concomitant CRISPR/cas9 targeting of hnRNPC. For this study, cas9 transgenic THP-1 were nucleofected with combinations of control gRNA, ADAR gRNA or hnRNPC gRNA to elucidate the basis for synergistic interferon-stmulated gene induction by combined ADAR and hnRNPC targeting. As a control for interferon-stimulated gene induction, IFN-alpha treated THP-1 were included, as well. To investigate potential interferon inducing mechanisms, we quantified gene expression, intron expression as well as the expression of regions rich in adenosine-to-inosine editing clusters. In a second part, nuclear vs cytosolic distribution of RNA rich in adenosine-to-inosine clusters was investigated by sequencing of total RNA or RNA from cytosolic and nuclear extracts of ADAR and/or hnRNPC targeted cells.
In the first part of the study, STING-deficient, cas9 transgenic THP-1 were nucleofected with combinations of control, GFP-targeting, ADAR-targeting or hnRNPC-targeting gRNA and cells collected for total RNA extraction on days three, four and five after nucleofection. In addition, another control-nucleofected sample was treated on day 3 for 24 h. The experiment was repeated three times leading to three replicates per condition. In the second part, WT cas9-transgenic THP-1 were nucleofected with combinations of control, ADAR-targeting or hnRNPC-targeting gRNA and cells were either collected for total RNA extraction or separated into digitonin-soluble (cytosolic) and digitonin-resistant (nuclear and mitochondrial) compartments and then RNA extracted. The experiment was repeated twice leading to two replicates per condition.
Differential gene expression analysis confirmed synergistic induction of interferon-stimulated genes. RNA-seq analysis demonstrated dysregulation of Alu-containing introns in hnRNPC-deficient cells via utilization of unmasked cryptic splice sites, including introns containing ADAR-dependent A-to-I editing clusters or regions enriched in editing clusters (ECRs) in general. These putative MDA5 ligands showed reduced editing in the absence of ADAR, providing a plausible mechanism for the combined effects of hnRNPC and ADAR. Part 2 of the study confirmed cytosolic access of a subset of ECRs to the cytosol.

overall_design: RNA-seq of THP-1 targeted with ADAR, hnRNPC or GFP gRNA or treated with IFN-alpha, total or cytosolic enriched RNA. Quantification of genes, introns, editing-cluster-rich regions or editing events.

first: Zia

last: Khan


title: CHIP-Seq analysis of CREB1 binding after ALVAC vaccination

first: Adam-Nicolas

last: Pelletier

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens


title: p38 MAP kinase signaling in microglia plays a sex-specific protective role in CNS autoimmunity and regulates microglial transcriptional states

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

summary:
Multiple sclerosis (MS) is an autoimmune demyelinating disease of the central nervous system, representing the leading cause of non-traumatic neurologic disease in young adults. This disease is three times more common in women, yet more severe in men, but the mechanisms underlying these sex differences remain largely unknown. MS is initiated by autoreactive T helper cells, but CNS-resident and CNS-infiltrating myeloid cells are the key proximal effector cells regulating disease pathology. We have previously shown that genetic ablation of p38α MAP kinase broadly in the myeloid lineage is protective in the autoimmune model of MS, experimental autoimmune encephalomyelitis (EAE), but only in females, and not males. To precisely define the mechanisms responsible, we used multiple genetic approaches and bone marrow chimeras to ablate p38α in microglial cells, peripheral myeloid cells, or both. Deletion of p38α in both cell types recapitulated the previous sex difference, with reduced EAE severity in females. Unexpectedly, deletion of p38α in the periphery was protective in both sexes. In contrast, deletion of p38α in microglia exacerbated EAE in males only, revealing opposing roles of p38α in microglia vs. periphery.
Bulk transcriptional profiling revealed that p38α regulated the expression of distinct gene modules in male vs. female microglia. Single-cell transcriptional analysis of WT and p38α-deficient microglia isolated from the inflamed CNS revealed a diversity of complex microglial states, connected by distinct convergent transcriptional trajectories. Microglial p38α deficiency in males resulted in enhanced transition from homeostatic to disease-associated microglial states, with the downregulation of regulatory genes such as Atf3, Rgs1, Socs3, and Btg2, and increased expression of inflammatory genes such as Cd74, Trem2, and MHC class I and II genes. Taken together, these results reveal the presence of a p38α-dependent male-specific molecular pathway in microglia that is protective in CNS autoimmunity, suggesting that autoimmunity in males and females is driven by distinct cellular and molecular pathways, thus informing the design of novel future sex-specific therapeutic approaches.

overall_design: We performed bulk gene expression profiling in male and female WT and p38alpha MAPK (Mapk14)-deficient microglia during experimental autoimmune encephalomyelitis (EAE); Microglia were isolated from the CNS by FACS, followed by RNA extraction and microarray-based transcriptional profiling. The effect of p38 deficiency in males vs. females was determed through differential gene expression analysis

middle: N

first: Mahalia

last: McGill


title: Integrative multi-omics approach for mechanism of humidifier disinfectant-associated lung injury

status: Public on Jul 06 2021

city: Seoul

first: Soo-Jong

last: Hong

state: Seoul

address: Department of Medicine, 88, OLYMPIC-RO 43-GIL, SONGPA-GU

country: South Korea

institute: University of Ulsan Collage of Medicine


title: Gene expression modulation in human dermal substitute exposed to reversible electroporation (ECT or GET types)

city: Toulouse

first: Laure

last: Gibot

address: 118 route de Narbonne

department: University Paul Sabatier

institute: CNRS

summary:
In this project we aimed at deciphering modulation in genes expression induced by external pulsed electric fields applied in reversible electroporation-based treatments. Thanks to their local application and transient effects, physical stimuli appear as attractive tools to remodel extracellular matrix, which was the point of interest in our to be published study. We assessed the potential of pulsed electric field technology, classically applied to drug delivery, to induce collagen remodeling at the tissue scale. A sophisticated in vitro tissue-engineered human dermal substitute, a tissue model rich in endogeneous extracellular matrix such as collagens, was used to demonstrate the effects of microsecond and millisecond pulsed electric fields applied respectively in electrochemotherapy (ECT) treatment and gene electrotransfer (GET) strategy. Our analyses, focused on matrisome genes and extracellular matrix remodeling, underpin that pulsed electric fields, a technology already approved for clinical use combined with anti-cancer agents, are particularly promising to provide local and effective treatment of abnormal extracellular matrix.
Part of this dataset was used to describe how pulsed electric field on its own (with no addition of external drugs) induce extracellular matrix (ECM) remodeling at human dermal scale, by focusing at genes related to matrisome subset. In this manuscript to be published, electrochemotherapy (ECT) parameters were named SP for "short pulses" and gene electrotransfer (GET) parameters were named LP for "long pulses". W demonstrated that these both types of electric parameters inducing reversible electroporation of the cells whitin the dermal tissue substitute induced 1) a rapid modulation (4h after electrostimulation) of mRNA’s genes composing the matrisome, particularly a down-regulation of pro-collagens and ECM maturation’s enzymes such as transglutaminase TG2 and LOX-like; 2) a transient decrease in pro-collagens production and hydroxyproline tissue content within a week after electrostimulation; 3) a long-lasting ROS-dependent over-activation of MMPs for at least 48h and 4) a down-regulation at both mRNA and protein level of pro-fibrotic TGF-β.

overall_design:
3 distinct conditions were produced and analyzed, each with 4 independant biological replicates. The first condition is the control condition (CTL) used as reference. The second one is a treatment using electric parameters applied in electrochemotherapy treatment (ECT) consisting in 8 pulses lasting 100µs, at 1000V/cm at a 1 Hz frequecy. The third condition is a treatment using electric parameters applied in gene electrotransfer (GET) consisting in 10 pulses lasting 5ms, at 600V/cm at a 1 Hz frequency. Please note that for conditions consisting in pulsed electric field application no additional drug was added, only the electric parameters.

Grant  number: ANR-17-CE19-0013-01
Grantee: Laure Gibot
Funding source: Agence Nationale de la Recherche

first: Sara

last: Gouarderes


title: Single-cell RNA sequencing reveals the novel role of Ezh2 in NK cell maturation and function

status: Public on Jul 07 2021

city: beijing

first: Minghang

last: Yu

address: No.10 Xitoutiao, You An Men

institute: Capital Medical University

summary: Our previous work indicated that the Enhancer of Zeste Homolog 2 (Ezh2) is a negative regulator of NK cell early differentiation and function by trimethylation of histone H3 lysine 27 (H3K27me3). Here, we deleted Ezh2 from immature NK and downstream progeny to explore its role in NK cell maturation by single-cell RNA sequencing (scRNA-seq). We identified six distinct NK stages based on transcriptional signature during the maturation of NK cells. Conditional deletion of Ezh2 in NK cells resulted in the maturation trajectory of NK cell arrested in CD11b SP stage 5 which is clustered with genes related to activating function of NK cells. Mechanistically, we speculated that Ezh2 plays a critical role in NK development by activating gene expression of the AP-1 superfamily independent of PRC2 function. Our results implied a novel role for the Ezh2-AP-1-Klrg1 axis to alter NK cell maturation trajectory and NK cell-mediated cytotoxicity.

overall_design: single-cell RNA seq of spleen NK cells from 6~8 week  old wild type (WT) and Ezh2ΔNK mice

first: Ziyang

last: Su

first: Xuefeng

last: Huang

first: Xi

last: Wang


title: RNA-Seq analysis of WT and BbTdp1 disruption strain in Beauveria bassiana

city: JiNan

first: ze

address: GuYunHu

institute: QiLu university of technology

summary: BbTdp1 is a novel protein with the function of regulating conidium and blastospore yields, fungal morphological changes and pathogenicity in Beauveria bassiana.

overall_design: Transcriptome comparison of wild type （WT）and  BbWor1 disruption type in Beauveria bassiana

first: Lei

last: Qiu

first: Ze

first: Li

last: Zhang

first: Tong-Sheng

first: Shun-Juan

last: Hu

first: Ji-Zheng

last: Song

first: Jia-Hua

last: Liu

first: Jing

first: Juan-Juan

first: Wen

last: Cheng


title: Integrative multi-omics approach for mechanism of humidifier disinfectant-associated lung injury [human]

first: Soo-Jong

summary: Inhalation of toxic chemicals, including recent e-cigarettes, often cause life-threatening lung injury. Although exposure to polyhexamethylene guanidine (PHMG)-containing humidifier disinfectant (HD) has been identified as a cause of fatal lung injury, the mechanism underlying HD-associated lung injury (HDLI) is unknown. The present study evaluated global changes in gene expression in lung tissues from patients with PHMG-induced HDLI, and compared gene expression changes in PHMG-induced rat lung tissues. Significantly different expressions in lung tissues between patients with HDLI and unaffected controls were observed. Furthermore, several fibrosis-associated overlapping genes (such as MMP2 and COL1A2) shared between humans with HDLI and rats exposed to PHMG were identified. Interactome network analysis predicted different pathways between children and adults with HDLI: the TGFβ/SMAD signaling pathway was central in adults, whereas other pathways, including integrin signaling, were associated with HDLI in children. Further interactome network analysis revealed that Rap1 and CCKR signaling pathways were significantly enriched in HDLI compared with idiopathic pulmonary fibrosis as well as their recapitulation in the lung tissues of rats exposed to PHMG. Our results suggest that MMP2-mediated different mechanisms between children and adults may be associated with PHMG-induced HDLI development, and Rap1 and CCKR pathways appear to be crucial.

overall_design: 19 formalin-fixed paraffin-embedded (FFPE) lung tissues from nine patients with HDLI and 10 FFPE from the adjacent normal tissues of lung tumors for controls

first: Jeong-Hyun

last: Kim

first: Kwoneel

first: Jeonghun

last: Yeom

first: Eun

last: Lee

first: Mi-Jin

last: Kang

first: Seung-Hwa

first: Kyunggon

first: So-Yeon

first: Sang-Bum

first: Dong

last: Oh

first: Kyuhong

first: Seong-Jin

last: Choi

last: Yang


title: Molecular mechanism of negative pressure irrigation inhibiting root growth and improving water use efficiency in maize

city: Daqing

first: jili

last: zhang

address: 5 Xinfeng Road

institute: heilongjiang bayi agricultural university

summary: NPI enriched more down-regulation genes involved in starch and sucrose metabolism, phenylpropanoid biosynthesis, amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis pathway, leading to restricted root growth. Three GO terms including channel activity, water transport, and water channel activity caused a high degree of gene enrichment. Thirteen genes related to water absorption and transport such as ZM00001D003006, ZM00001D014285 et al. were highly up-regulated, which might be the key genes for the significant increase in water use efficiency of maize under negative pressure irrigation.

overall_design: Monitoring of different genes under different irrigation methods

first: Jili

first: Peng

first: Haiyu

last: Long


title: Mesomelic Dysplasias Associated With The HOXD Locus Are Caused By Regulatory Reallocations [scRNA-seq]

status: Public on Jul 20 2021

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

institute: EPFL

summary: Some human families display severe shortening and bending of the radius and ulna, a condition referred to as mesomelic dysplasia. Many of these families contain chromosomal rearrangements at 2q31, where the human HOXD locus maps. In mice, the dominant X-ray-induced Ulnaless inversion of the HoxD gene cluster produces a similar phenotype suggesting that the same pathological mechanism is at work in humans and mice. A tentative hypothesis was proposed where the various alterations to the genomic structure of HOXD could translocate Hoxd13 near to proximal limb enhancers, leading to its deleterious gain-of-expression in the embryonic forelimb. We evaluated this hypothesis by engineering a ca. 1Mb large inversion including the HoxD gene cluster, in order to position Hoxd13 within a chromatin domain rich in proximal limb enhancers. We show that these enhancers contact and activate Hoxd13 in proximal cells, concomitant to the formation of a mesomelic dysplasia phenotype. A secondary mutation in the coding frame of the HOXD13 protein in-cis with the inversion completely rescued the limb alterations, demonstrating that ectopic HOXD13 is indeed the unique cause of this bone anomaly. Single cell expression analysis and evaluation of HOXD13 binding sites in cells from this ectopic expression domain suggests that the phenotype arises primarily by acting through genes normally controlled by HOXD13 in distal limb cells. Altogether, these results provide a conceptual and mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.

overall_design: Embryos were collected and stored in 1X PBS treated with DEPC and held on ice while genotyping was performed. Embryos with the desired genotype were selected and the posterior portion of each of the forelimbs was isolated for each replicate. The cells were digested in collagenase and stored in 1X PBS containing 10% FCS and 0.2mM EDTA to prevent cellular aggregation. GEM formation was performed with 10X protocol according to the 3.1 chemistry protocol.

first: Christopher

middle: C

last: Bolt

first: Bénédicte

last: Mascrez

first: Denis

last: Duboule


title: The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation [ATAC-seq]

status: Public on Aug 04 2021

city: Stanford

first: Daniel

middle: Sunwook

address: 269 Campus Drive, CCSR 2150

institute: Stanford School of Medicine

summary: A deep-learning framework interprets multi-omic data across epidermal differentiation, identifying cooperative DNA sequence rules that regulate gene modules. Massively parallel reporter analysis validates temporal dynamics and cis-regulatory logic.

middle: S

first: Viviana

last: Risca

first: Arwa

last: Kathiria


title: Predictive Models of Drug Response in Canine Osteosarcoma: A Prospective Clinical Trial Testing the COXEN Approach

city: Fort Collins

first: Sunetra

last: Das

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: This was a prospective clinical trial testing the ability of gene expression models of drug sensitivity that were developed in human and canine cell lines and applied to outcomes in dogs treated with adjuvant carboplatin and/or doxorubicin. Tumor samples were collected prospectively, and gene expression analysis was conducted using Affymetrix Canine Genome 2.0 Arrays.

overall_design: Tumor biopsy samples were collected using a Michele Trephine bone biopsy instrument and were reviewed by a veterinary pathologist for assessment of viable tumor present from each sample. Two samples from each tumor with the highest percent viable tumor were selected for mRNA isolation and subsequent Affymetrix Canine 2.0 microarray analysis.

last: Gustafson

first: Dawn

last: Duval


title: REV-ERB nuclear receptors in the suprachiasmatic nucleus control circadian period and restrict diet-induced obesity

status: Public on Jul 15 2021

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

summary: Circadian disruption, as shift work, is associated with metabolic diseases, including obesity and fatty liver, often attributed to discordance between internal clocks and environmental timekeepers1-5. However, this desynchrony hypothesis has not been rigorously tested. The body’s master clock, located in the suprachiasmatic nucleus (SCN), synchronizes peripheral clocks and ultimately metabolism2,6. Molecular clocks are comprised of transcriptional translational feedback loops involving gene activation by BMAL1, which is rhythmically repressed by separate mechanisms involving PER/CRY and REV-ERB nuclear receptors. Mice harboring whole body deletion of REV-ERBa/b have been reported to be arrhythmic7. However, we report here that mice lacking REV-ERBs specifically in the SCN maintain free-running and metabolic rhythms, but these are strikingly shortened by nearly 3 hours. When housed under a 24 hours light-dark cycle and fed an obesogenic diet, these mice gained excess weight and accrued more liver fat than controls. Remarkably, these metabolic disturbances were corrected by matching environmental lighting to the shortened endogenous clock period. Thus, SCN REV-ERBs are not required to maintain rhythmicity but powerfully control the free-running period. Moreover, these results support the hypothesis that dissonance between environmental conditions and endogenous period causes metabolic disruption. This has important implications for chronotherapy of metabolic and behavioral disorders.

overall_design: Transcriptomic profiling (RNA-seq) of punched-out suprachiasmatic nuclei (SCN)  harvested from control or REV-ERBS (alpha and beta) DKKO mice collected during at CT4 or CT16. Library was prepared with Illumina Truseq kit and sequenced on  Illumina Hiseq 4000 sequencer.

first: Marine

last: Adlanmerini

first: Mitchell

last: Lazar


title: Temporal controls over interareal cortical projection neuron fate diversity (MAPseq)

status: Public on Jul 01 2021

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

institute: University of Geneva

summary: Interconnectivity between neocortical areas is critical for sensory integration and sensorimotor transformations. These functions are mediated by heterogeneous interareal cortical projection neurons (ICPN), which send axon branches to distinct cortical areas as well as to subcortical targets. Although ICPN are anatomically diverse, they are molecularly homogeneous and how the diversity of their anatomical and functional features emerge during development remains largely unknown. Here, we address this question by linking connectome and transcriptome in developing single ICPN of the mouse neocortex using a combination of MAPseq mapping (to identify single-neuron axonal projections) and single-cell RNA sequencing (to identify corresponding gene expression). Focusing on neurons of the primary somatosensory cortex (S1), we reveal a protracted unfolding of the molecular and functional differentiation of motor cortex-projecting (M) compared to secondary somatosensory cortex-projecting (S2) ICPN. We identify SOX11 as a temporally differentially expressed transcription factor in M vs. S2 ICPN. Postnatal manipulation of SOX11 expression level in S1 impaired sensorimotor connectivity and selectively disrupted exploratory behavior in freely moving mice. Together, our results reveal that within a single cortical area, different subtypes of ICPN have distinct postnatal molecular differentiation paces, which is then reflected in distinct circuit connectivities and functions. Dynamic differences in expression levels of largely generic set of genes, rather than fundamental differences in the identity of developmental genetic programs, may thus account for emergence of intra-type diversity in cortical neurons.

overall_design: This record contains mapseq data from P14, P5, P7 mouse cortex in quadruplicate. A 32bp-barcoded sindbis virus is injected in the primary somatosensory cortex S1. The virus enter the neurons, replicate and migrate to the terminal connections. Then, S1 injection area and 6 projection targets where S1 cells are expected to project are dissected (A, C, M, S2, Sub, V). Barcodes of the Sindbis viruses are sequenced by bulk RNA-seq for each area so that we can link S1-cells to their projection targets.

first: Esther

last: Klingler

first: Ugo

last: Tomasello

first: Justus

last: Kebschull

first: Alessandro

last: Contestabile

first: Gregorio

last: Galiñanes

first: Sabine

last: Fièvre

last: Huber

first: Alexandre

last: Dayer

first: Camilla

last: Bellone

first: Antonio

last: Santinha

first: Randall

last: Platt

last: Jabaudon


title: A novel DNA methylation signature in Merkel Cell Carcinoma

status: Public on Jul 13 2021

city: Los Angeles

first: Gangning

last: Liang

address: 1441 Eastlake Ave. NOR7344

department: Urology

institute: University f Southern California

type: Methylation profiling by genome tiling array

summary: Merkel cell carcinoma (MCC) is a rare but aggressive skin cancer with neuroendocrine features. Although the role of epigenetic in tumorigenesis has been documented in most type of cancer, it is overlooked in MCC. The treatment options for MCC is limited and the five-year survival rate remains as low as 33%. In addition, recent studies have suggested multiple mechanisms of epigenetic dysregulation that may contribute to loss H3K27me3 and the tumorigenesis in MCC but not well studied.                                  In this study, we conducted DNA methylation analysis of an existing retrospective cohort of clinically annotated MCC samples, which included samples from 8 primary tumors, three metastatic skin tumors, four metastatic lymph node tumors, and five paired normal tissue samples. Global DNA methylation profile was performed using Illumina Infinium MethylationEPIC array. Two MCC cell lines were also analyzed for DNA methylation and gene expression (RNA-seq) to confirm the correlation between DNA methylation and gene expression for MCC.                                                                                Our analysis revealed 24,497 loci (14,456 genes) that showed significantly different DNA methylation pattern in the four groups (ANOVA p-value < 0.05 and standard deviation of mean of groups > 0.25) namely adjacent normal, primary tumor, metastatic skin, and metastatic lymph node in MCC patients. By GO terms analysis, the genes correlated with DNA methylation alteration associated with nervous system, cell adhesion, signal transduction, and development pathways. We also observed 870 probes differentially methylated in MCPyV positive and MCPyV negative tumor (FDR adjusted p-value < 0.05 and delta change greater than 0.4 or less than -0.4). Furthermore, using expression and DNA methylation data from two MCC cell lines (MS1 and MCC13) as validation, we identified 964 MCC specific genes directly regulated by DNA methylation either at promoter or gene body, which are highly enriched in nervous system related pathways. By this approach, we not only identify DNA methylation markers for MCC and MCPyV status but also genes regulated by DNA methylation in MCC, MCPyV status, and neuroendocrine features. Most importantly, our results may also suggest overexpression of KDM6B and EZHIP by loss of DNA methylation in their promoter may contribute to loss of H3K27me3 in MCC. In addition, we observed the DNA methylation profile of MS1 resembled MCC patient sample, while DNA methylation profile of MCC13 cell line was similar to small cell lung carcinoma (SCLC), which suggested that MCC13 cell line may originally come from SCLC.                                                                                Taken together, we have demonstrated dramatic DNA methylation alteration along with four unique patterns in normal, primary and metastatic MCC. Our finding provides DNA methylation markers not only for diagnosis or prognosis of MCC and MCPyV status but also correlate gene expression status of MCC specific genes with important functional roles in MCC tumorigenesis, MCPyV expression, neuroendocrine feature and H3K27me3 status. The identification of DNA methylation alteration in MCC also provides foundation for potential implication of epigenetic therapy for MCC patients.

overall_design: 20 samples: 5 normal; 8 primary; 4 Metastatic lymph node; 3 Metastatic skin

first: Hemant

last: Gujar

first: Daniel

middle: J

last: Weisenberger

first: Yvonne

last: Tsai

first: Arjun

last: Mehta


title: The H3K36me2 writer-reader dependency in H3K27M-DIPG

city: Washington

first: Jia-Ray

last: Yu

state: DC

address: 7144 13th Pl Nw

institute: FBRI at Virginia Tech Carilion

summary: The lysine-to-methionine mutation at residue 27 of histone H3 (H3K27M) is a driving mutation in Diffuse Intrinsic Pontine Glioma (DIPG), a highly aggressive form of pediatric brain tumor with no effective treatment and little chance of survival. H3K27M reshapes the epigenome through a global inhibition of PRC2 catalytic activity, displacement of methylation at lysine 27 of histone H3 (H3K27me2/3), and thus promoting oncogenesis of DIPG. As a consequence, a histone modification H3K36me2, antagonistic to H3K27me2/3, is aberrantly elevated. Here, we investigate the role of H3K36me2 in H3K27M-DIPG by tackling its upstream catalyzing enzymes (writers) and downstream binding factors (readers). We determine that NSD1 and NSD2 are the key writers for H3K36me2. Loss of NSD1/2 in H3K27M-DIPG impedes cellular proliferation in vitro and tumorigenesis in vivo, and disrupts tumor-promoting gene expression programs. Further, we demonstrate that LEDGF and HDGF2 are the main readers that mediate the pro-tumorigenic effects downstream of NSD1/2-H3K36me2. Treatment with a chemically modified peptide mimicking endogenous H3K36me2 dislodges LEDGF/HDGF2 from chromatin and specifically inhibits the proliferation of H3K27M-DIPG. Together, our results indicate a functional pathway of NSD1/2-H3K36me2-LEDGF/HDGF2 as an acquired dependency in H3K27M-DIPG and suggest a possibility to target this pathway for therapeutic interventions.

overall_design: Examination of genomic distribution of HDGF2 and LEDGF

first: Danny

last: Reinberg


title: Temporal controls over interareal cortical projection neuron fate diversity (retrobeads)

first: Julien

last: Prados

overall_design: This record contains single cell transcriptomics data from one Fluidigm integrated fluidic circuits. Retrobeads are injected in cerebral cortex M1 and S2 of P9 mouse. Primary somatosensory cortex is dissected and FACS-sorted to select for cells with retrobeads that project either to M1 or S2. The transcriptome of these S1 cells is sequenced with using Fluidigm integrated fluidic circuits on C1 system. The goal of this experiment is to determine genes patterns of cells projecting to either M1 or S2.

first: Klingler

last: Esther

last: Tomasello

last: Kebschull

first: Jabaudon

last: Denis